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Crystal structure of the receiver domain of the histidine kinase CKI1 from Arabidopsis thaliana complexed with Mg2+ and BeF3-
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.05 289 2.54 M (NH4)2(SO4), 0.1 M MES pH 5.05, 12% glycerol
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.85 α = 90 b = 100.152 β = 90 c = 80.139 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL PSI PILATUS 6M 2014-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.05 46.74 99.9 0.05 1 20.5 6.5 13705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 99.9 0.47 0.945 4.1 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3MM4 2.05 42.47 13028 658 99.91 0.18378 0.18175 0.1945 0.22515 0.2239 RANDOM 46.22
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 3.23 -0.15 -3.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.178 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 16.178 r_long_range_B_other 11.301 r_long_range_B_refined 11.288 r_scangle_other 9.337 r_scbond_other 6.22 r_scbond_it 6.212 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.178 r_dihedral_angle_4_deg 22.273 r_dihedral_angle_3_deg 16.178 r_long_range_B_other 11.301 r_long_range_B_refined 11.288 r_scangle_other 9.337 r_scbond_other 6.22 r_scbond_it 6.212 r_dihedral_angle_1_deg 6.029 r_mcangle_it 5.479 r_mcangle_other 5.478 r_mcbond_it 4.159 r_mcbond_other 4.15 r_angle_refined_deg 1.85 r_angle_other_deg 1.02 r_chiral_restr 0.158 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1160 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing